rs11568514

chr5-132392510-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM1 PM2 PP3 PP5 BP4

The NM_003060.4(SLC22A5):c.1345T>G(p.Tyr449Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000203 in 1,614,180 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y449C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0011 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: SLC22A5 NM_003060.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:7
• Conservation: PhyloP100: 4.74

Genes affected

SLC22A5 (HGNC:10969): (solute carrier family 22 member 5) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is a plasma integral membrane protein which functions both as an organic cation transporter and as a sodium-dependent high affinity carnitine transporter. The encoded protein is involved in the active cellular uptake of carnitine. Mutations in this gene are the cause of systemic primary carnitine deficiency (CDSP), an autosomal recessive disorder manifested early in life by hypoketotic hypoglycemia and acute metabolic decompensation, and later in life by skeletal myopathy or cardiomyopathy. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_003060.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: Multiple lines of computational evidence support a deleterious effect 8: AlphaMissense, BayesDel_noAF, Cadd, Eigen, MutationAssessor, PrimateAI, PROVEAN, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• PP5: Variant 5-132392510-T-G is Pathogenic according to our data. Variant chr5-132392510-T-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 25420.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=7, Likely_pathogenic=1, Pathogenic=4}. Variant chr5-132392510-T-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.104227066).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A5	NM_003060.4	c.1345T>G	p.Tyr449Asp	missense_variant	8/10	ENST00000245407.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A5	ENST00000245407.8	c.1345T>G	p.Tyr449Asp	missense_variant	8/10	1	NM_003060.4	P1

Frequencies

GnomAD3 genomes AF: 0.00109 AC: 166 AN: 152218 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00376

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000254 AC: 64 AN: 251478 Hom.: 0 AF XY: 0.000177 AC XY: 24 AN XY: 135910

Gnomad AFR exome AF: 0.00381

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000111 AC: 162 AN: 1461844 Hom.: 0 Cov.: 32 AF XY: 0.0000990 AC XY: 72 AN XY: 727228

Gnomad4 AFR exome AF: 0.00430

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.000232

GnomAD4 genome AF: 0.00108 AC: 165 AN: 152336 Hom.: 1 Cov.: 32 AF XY: 0.000993 AC XY: 74 AN XY: 74500

Gnomad4 AFR AF: 0.00373

Gnomad4 AMR AF: 0.000457

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000171 Hom.: 0

Bravo AF: 0.00122

ESP6500AA AF: 0.00363 AC: 16

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000288 AC: 35

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Renal carnitine transport defect Pathogenic:4 Uncertain:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 31, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jul 26, 2016	The SLC22A5 c.1345T>G (p.Tyr449Asp) variant is a missense variant that has been reported in a total of three individuals with systemic primary carnitine deficiency, including in one who carried the variant in a compound heterozygous state and in one who carried the variant in a heterozygous state with an unidentified second variant. The third individual was heterozygous but also carried a variant in the VLCAD gene, which is associated with very-long-chain acyl-CoA dehydrogenase deficiency, a disease with phenotypic overlap to systemic primary carnitine deficiency (Amat di San Filippo and Longo 2004; Li et al. 2010). The p.Tyr449Asp variant was reported in a heterozygous state in one of 270 ethnically diverse healthy volunteers (Urban et al. 2006) and is reported at a frequency of 0.00605 in the African population of the 1000 Genomes Project. Functional studies in CHO cells (Amat di San Filippo and Longo 2004; Amat di San Filippo et al. 2008) and HEK 293 cells (Urban et al. 2006) indicate the variant impairs carnitine transport, reduces sodium stimulation of the channel, and affects substrate specificity but does not affect membrane localization or the kinetic constant of the channel. Based on the evidence, the p.Tyr449Asp variant is classified as a variant of unknown significance but suspicious for pathogenicity for systemic primary carnitine deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genomics Program, Stanford Medicine	Mar 30, 2021	• The p.Tyr449Asp variant in the SLC22A5 gene has been previously reported in at least 6 individuals with systemic primary carnitine deficiency (Li et al., 2010; Vockley et al., 2000; Amat di San Filippo et al., 2004; Frigeni et al., 2017; Guevara-Campos et al., 2019). In one individual, this variant was observed in trans with another likely pathogenic/pathogenic variant (p.Leu269Argfs*26); and another individual was homozygous for this variant, consistent with autosomal recessive inheritance (Frigeni et al., 2017; ARUP Primary Carnitine Deficiency and SLC22A5 Database). • The p.Tyr449Asp variant has been identified in 92/24,958 African/African-American chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). • Functional studies of this variant are supportive of a deleterious effect to the protein; however, it is unclear if this would be sufficient to be disease-causing (Amat di San Filippo et al., 2004; Urban et al., 2006; Frigeni et al., 2017). • The p.Tyr449Asp variant is located in the intracellular loop between transmembrane domains 10 and 11 of SLC22A5 (Amat di San Filippo et al., 2004). Other nearby disease-associated variants have been described in this domain, including at least one that has been shown to reduce carnitine transport (Wang et al., 2000). • Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. • These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Tyr449Asp variant as likely pathogenic for systemic primary carnitine deficiency in an autosomal recessive manner based on the information above. [ACMG evidence codes used: PS3_moderate; PM3; PM1; PP3] -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change replaces tyrosine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 449 of the SLC22A5 protein (p.Tyr449Asp). This variant is present in population databases (rs11568514, gnomAD 0.4%). This missense change has been observed in individual(s) with primary carnitine deficiency (PMID: 28841266; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 25420). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC22A5 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects SLC22A5 function (PMID: 14665638, 16652335, 16931768, 18337137). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	in vitro;research	Giacomini Lab, University of California, San Francisco	Oct 03, 2022	- -

not provided Pathogenic:1 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 29, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 12, 2021	Reported in an individual with 12.4% carnitine transport activity in fibroblasts who also harbored a frameshift variant in SLC22A5, however it is not known whether the two variants occurred on the same (in cis) or opposite (in trans) allele (Frigeni et al., 2017); Reported in two individuals who were heterozygous for this single variant in SLC22A5 (Dobrowolski et al., 2005; Amat di San Filippo and Longo, 2004); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Published expression studies are conflicting as to whether the Y449D variant reduces carnitine transport to a level expected to be pathogenic (Amat di San Filippo and Longo, 2004; Urban et al., 2006); This variant is associated with the following publications: (PMID: 31980526, 28841266, 31200524, 16931768, 14665638, 18337137, 16602102, 16652335, 18673259, 19940846, 20574985, 23757202, 25087612, 15714519, 23379544, 26828774) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 04, 2017	The SLC22A5 c.1345T>G, p.Tyr449Asp variant (rs11568514) has been reported in individuals with primary carnitine deficiency (Amat di San Filippo 2004, Li 2010). Functional characterization of the variant protein indicates a decrease in carnitine transport in response to sodium, and an altered preference for tetraethylammonium cation (Amat di San Filippo 2004, Urban 2006). The p.Tyr449Asp variant is located in the intracellular loop between transmembrane domains 10 and 11, and another alteration in this region (p.Glu452Lys) have also been shown to affect sodium-dependent carnitine transport (Wang 2000), suggesting that this region has functional significance. The variant is listed as pathogenic in ClinVar (Variation ID: 25420), and observed in the general population databases at a frequency of 0.2 percent in the 1000 Genomes Project (8/5008 alleles), 0.1 percent in the Exome Variant Server (16/13006 alleles), and 0.03 percent in the Genome Aggregation Database (90/277216 alleles). The tyrosine at residue 449 is moderately conserved, and computational algorithms (Align GVGD, Mutation Taster, PolyPhen-2, SIFT) predict that the variant has an impact on the protein. Based on the above information, the variant is classified as pathogenic. References: Amat di San Filippo C et al. Tyrosine residues affecting sodium stimulation of carnitine transport in the OCTN2 carnitine/organic cation transporter. J Biol Chem. 2004; 279(8):7247-53. Li F et al. Molecular spectrum of SLC22A5 (OCTN2) gene mutations detected in 143 subjects evaluated for systemic carnitine deficiency. Hum Mutat. 2010; 31(8):E1632-51. Urban T et al. Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5). Mol Pharmacol. 2006; 70(5):1602-11. Wang Y et al. Abnormal sodium stimulation of carnitine transport in primary carnitine deficiency. J Biol Chem. 2000; 275(27):20782-6. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Mar 31, 2017	- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 23, 2022

Variant summary: SLC22A5 c.1345T>G (p.Tyr449Asp) results in a non-conservative amino acid change located in the Major facilitator superfamily domain (IPR020846) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00025 in 251478 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in SLC22A5 causing Systemic Primary Carnitine Deficiency (0.00025 vs 0.0046), allowing no conclusion about variant significance. c.1345T>G has been reported in the literature as a non-informative genotype (second allele not specified) and at-least one compound heterozygous genotype in individuals affected with features of Systemic Primary Carnitine Deficiency (example, Amat di San Fillippo_2004, Dobrowlski_2005, Frigeni_2017). One recent report details an individual with a heterozygous genotype in whom this variant is discussed a risk factor for autism. However, to our knowledge, this individual did not present with classical features of Primary Carnitine Deficiency/Carnitine transport defect (example, Guevara-Campos_2019). These data do not allow any conclusion about variant significance. Multiple publications report experimental evidence evaluating an impact on protein function (example, Amat di San Fillippo_2004). The most pronounced variant effect results in 18% of normal carnitine transporter activity in-vitro. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (Pathogenic, n=2; VUS, n=6). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

See cases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Jun 22, 2021

ACMG classification criteria: PM2, PP3, BP1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.90
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Pathogenic	0.42
Cadd	Pathogenic	29
Dann	Uncertain	0.99
DEOGEN2	Pathogenic	0.84	D;.
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.87	D;T
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.10	T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	H;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-7.1	D;D
REVEL	Pathogenic	0.85
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0040	D;D
Polyphen		1.0	D;.
Vest4		0.91
MVP		1.0
MPC		1.1
ClinPred		0.34	T
GERP RS		6.2
Varity_R		0.97
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11568514; hg19: chr5-131728202;